@article{liebe2010abcpy,
	author = {Liepe, Juliane and Barnes, Chris and Cule, Erika and Erguler, Kamil and Kirk, Paul and Toni, Tina and Stumpf, Michael P.H.}, 
	title = {ABC-SysBio approximate Bayesian computation in Python with GPU support},
	volume = {26}, 	
	number = {14}, 
	pages = {1797-1799}, 
	year = {2010}, 
	doi = {10.1093/bioinformatics/btq278}, 
	URL = {http://bioinformatics.oxfordjournals.org/content/26/14/1797.abstract}, 
	eprint = {http://bioinformatics.oxfordjournals.org/content/26/14/1797.full.pdf+html}, 
	journal = {Bioinformatics} 
}

@article{toni2009abc,
	author = {Toni, Tina and Welch, David and Strelkowa, Natalja and Ipsen, Andreas and Stumpf, Michael P.H}, 
	title = {Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems},
	volume = {6}, 
	number = {31}, 
	pages = {187-202}, 
	year = {2009}, 
	doi = {10.1098/rsif.2008.0172}, 
	URL = {http://rsif.royalsocietypublishing.org/content/6/31/187.abstract}, 
	eprint = {http://rsif.royalsocietypublishing.org/content/6/31/187.full.pdf+html}, 
	journal = {Journal of The Royal Society Interface} 
}

@article{filippi2011optimal,
   author = {{Filippi}, S. and {Barnes}, C. and {Cornebise}, J. and {Stumpf}, M.~P.~H },
    title = "{On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo}",
    journal = {ArXiv e-prints},
   archivePrefix = "arXiv",
   eprint = {1106.6280},
  primaryClass = "stat.CO",
   keywords = {Statistics - Computation},
   year = 2011,
   month = jun,
   adsurl = {http://adsabs.harvard.edu/abs/2011arXiv1106.6280F},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@article{daniels2008sloppiness,
  title={Sloppiness, robustness, and evolvability in systems biology},
  author={Daniels, B.C. and Chen, Y.J. and Sethna, J.P. and Gutenkunst, R.N. and Myers, C.R.},
  journal={Current opinion in biotechnology},
  volume={19},
  number={4},
  pages={389--395},
  year={2008},
  publisher={Elsevier}
}

@article{das2012dupl,
   author = {{Dasmahapatra}, S.},
    title = "{Model of haplotype and phenotype in the evolution of a duplicated autoregulatory activator}",
  journal = {ArXiv e-prints},
archivePrefix = "arXiv",
   eprint = {1212.0795},
 primaryClass = "q-bio.MN",
 keywords = {Quantitative Biology - Molecular Networks, Physics - Biological Physics, Quantitative Biology - Populations and Evolution},
     year = 2012,
    month = dec,
   adsurl = {http://adsabs.harvard.edu/abs/2012arXiv1212.0795D},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@ARTICLE{pfeuty2011robust,
   author = {{Pfeuty}, B. and {Thommen}, Q. and {Lefranc}, M.},
    title = "{Robust Entrainment of Circadian Oscillators Requires Specific Phase Response Curves}",
  journal = {Biophysical Journal},
archivePrefix = "arXiv",
   eprint = {1012.1521},
 primaryClass = "q-bio.QM",
     year = 2011,
    month = jun,
   volume = 100,
    pages = {2557-2565},
      doi = {10.1016/j.bpj.2011.04.043},
   adsurl = {http://adsabs.harvard.edu/abs/2011BpJ...100.2557P},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@article{Moles2003param,
	author = {Moles, Carmen G. and Mendes, Pedro and Banga, Julio R.}, 
	title = {Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods},
	volume = {13}, 
	number = {11}, 
	pages = {2467-2474}, 	
	year = {2003}, 
	doi = {10.1101/gr.1262503}, 
	URL = {http://genome.cshlp.org/content/13/11/2467.abstract}, 
	eprint = {http://genome.cshlp.org/content/13/11/2467.full.pdf+html}, 
	journal = {Genome Research} 
}

@article{lipinski2011high,
  title={High Spontaneous Rate of Gene Duplication in< i> Caenorhabditis elegans</i>},
  author={Lipinski, K.J. and Farslow, J.C. and Fitzpatrick, K.A. and Lynch, M. and Katju, V. and Bergthorsson, U.},
  journal={Current Biology},
  volume={21},
  number={4},
  pages={306--310},
  year={2011},
  publisher={Elsevier}
}

@article{kirk2008parameter,
  title={Parameter inference for biochemical systems that undergo a Hopf bifurcation},
  author={Kirk, P.D.W. and Toni, T. and Stumpf, M.P.H.},
  journal={Biophysical journal},
  volume={95},
  number={2},
  pages={540},
  year={2008},
  publisher={The Biophysical Society}
}

@article{tyson2003sniffers,
  title={Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell},
  author={Tyson, J.J. and Chen, K.C. and Novak, B.},
  journal={Current opinion in cell biology},
  volume={15},
  number={2},
  pages={221--231},
  year={2003},
  publisher={Elsevier}
}

@article{lazebnik2002can,
  title={Can a biologist fix a radio?--Or, what I learned while studying apoptosis.},
  author={Lazebnik, Y.},
  journal={Cancer cell},
  volume={2},
  number={3},
  pages={179},
  year={2002}
}

@article{roenneberg2008modelling,
  title={Modelling biological rhythms},
  author={Roenneberg, T. and Chua, E.J. and Bernardo, R. and Mendoza, E.},
  journal={Current biology},
  volume={18},
  number={17},
  pages={R826--R835},
  year={2008},
  publisher={Elsevier}
}

@article{gonze2011modeling,
  title={Modeling circadian clocks: From equations to oscillations},
  author={Gonze, D.},
  journal={Central European Journal of Biology},
  volume={6},
  number={5},
  pages={699--711},
  year={2011},
  publisher={Springer}
}

@MISC{Walsh04markovchain,
    author = {B. Walsh},
    title = {Markov Chain Monte Carlo and Gibbs Sampling},
    year = {2004}
}

@book{gelman2003bayesian,
  title={Bayesian data analysis},
  author={Gelman, A. and Carlin, J.B. and Stern, H.S. and Rubin, D.B.},
  year={2003},
  publisher={Chapman \& Hall/CRC}
}

@article{konopka2010gene,
  title={Gene expression model (in) validation by Fourier analysis},
  author={Konopka, T. and Rooman, M.},
  journal={BMC systems biology},
  volume={4},
  number={1},
  pages={123},
  year={2010},
  publisher={BioMed Central Ltd}
}

@article{myers2007python,
  title={Python unleashed on systems biology},
  author={Myers, C.R. and Gutenkunst, R.N. and Sethna, J.P.},
  journal={Computing in Science \& Engineering},
  volume={9},
  number={3},
  pages={34--37},
  year={2007},
  publisher={IEEE}
}

@article{rosenfeld2002negative,
  title={Negative autoregulation speeds the response times of transcription networks},
  author={Rosenfeld, N. and Elowitz, M.B. and Alon, U. and others},
  journal={Journal of molecular biology},
  volume={323},
  number={5},
  pages={785--793},
  year={2002},
  publisher={London, New York, Academic Press.}
}

@article{marjoram2003markov,
  title={Markov chain Monte Carlo without likelihoods},
  author={Marjoram, P. and Molitor, J. and Plagnol, V. and Tavar{\'e}, S.},
  journal={Proceedings of the National Academy of Sciences},
  volume={100},
  number={26},
  pages={15324--15328},
  year={2003},
  publisher={National Acad Sciences}
}

@article{pritchard1999population,
  title={Population growth of human Y chromosomes: a study of Y chromosome microsatellites.},
  author={Pritchard, J.K. and Seielstad, M.T. and Perez-Lezaun, A. and Feldman, M.W.},
  journal={Molecular Biology and Evolution},
  volume={16},
  number={12},
  pages={1791--1798},
  year={1999},
  publisher={SMBE}
}

@article{bass2010circadian,
  title={Circadian integration of metabolism and energetics},
  author={Bass, J. and Takahashi, J.S.},
  journal={Science Signalling},
  volume={330},
  number={6009},
  pages={1349},
  year={2010},
  publisher={AAAS}
}

@article{becker2004modeling,
  title={Modeling feedback loops of the mammalian circadian oscillator},
  author={Becker-Weimann, S. and Wolf, J. and Herzel, H. and Kramer, A.},
  journal={Biophysical journal},
  volume={87},
  number={5},
  pages={3023--3034},
  year={2004},
  publisher={Elsevier}
}

@article{mirsky2009model,
  title={A model of the cell-autonomous mammalian circadian clock},
  author={Mirsky, H.P. and Liu, A.C. and Welsh, D.K. and Kay, S.A. and Doyle, F.J.},
  journal={Proceedings of the National Academy of Sciences},
  volume={106},
  number={27},
  pages={11107--11112},
  year={2009},
  publisher={National Acad Sciences}
}

@article{moles2003parameter,
  title={Parameter estimation in biochemical pathways: a comparison of global optimization methods},
  author={Moles, C.G. and Mendes, P. and Banga, J.R.},
  journal={Genome research},
  volume={13},
  number={11},
  pages={2467--2474},
  year={2003},
  publisher={Cold Spring Harbor Lab}
}

@article{olivier2002modelling,
  title={Modelling cellular processes with Python and Scipy},
  author={Olivier, BG and Rohwer, JM and Hofmeyr, J.H.S.},
  journal={Molecular biology reports},
  volume={29},
  number={1},
  pages={249--254},
  year={2002},
  publisher={Springer}
}

@Misc{scipy,
  author =    {Eric Jones and Travis Oliphant and Pearu Peterson and others},
  title =     {{SciPy}: Open source scientific tools for {Python}},
  year =      {2001--},
  url = "http://www.scipy.org/"
}

@book{lotka1925elements,
  title={Elements of physical biology},
  author={Lotka, A.J.},
  year={1925},
  publisher={Williams \& Wilkins Baltimore}
}

@article{del2012adaptive,
  title={An adaptive sequential Monte Carlo method for approximate Bayesian computation},
  author={Del Moral, P. and Doucet, A. and Jasra, A.},
  journal={Statistics and Computing},
  volume={22},
  number={5},
  pages={1009--1020},
  year={2012},
  publisher={Springer}
}